In any experiment concerning the nanoscale junction, such as in the STM, it is extremely important to have the tip-sample junction as same temperature. Normally, you can have this situation satisfied in the low temperature STM, where both the sample and tip are cooled using either L-N2 or L-He. both the tip and sample are within the cryostat in the design. Whereas the variable temperature STM, works under the principle of continuous flow cryostat, needs a continuous flow of Nitrogen or helium in order to maintain the sample cool. Even if the sample cools to low temperature, the tip will be ' mostly' at higher temperature. 

Generally, in the case of VT-STM, it is advisable to leave the tip scanning a cold surface ( Lets say Au(111) or Si(111) or similar) for long time, so that the tip-sample junction reaches an equilibrium temperature. 

Thank you very much for helping me out and clarifying my doubt. Can you please further elaborate the reasons for maintaining the tip and the sample at the same temperature.

The lower is the tip temperature, the smaller is the thermal broadening of the energy levels, the better is energy resolution of the LTSTM. In the VT-STM one mostly use the cryostat to cool down the sample in order to study physisorbed molecules/atoms/clusters i.e. the objects with low adsorption energy, that can otherwise be easily desorbed by the tip action.

Best